Matcher
Vilanova,David,LAUSANNE,NRC/BS
david.vilanova at rdls.nestle.com
Tue Nov 26 14:12:19 UTC 2002
Thanks Peter,
Sorry for the mistake.
I'm writing a bioperl script which automatically runs an emboss aplication.
I could have worked by generating foreach sequence I read a new file but it
looks pretty nice like that.
Regards,
David
#! /usr/bin/perl -w
use Bio::Factory::EMBOSS;
use Bio::SeqIO;
die "Usage: perl script.pl [seqfileA] [seqfileB] [outfile]\n" unless @ARGV
eq '3';
#Read input files
($seqfileA,$seqfileB,$outfile) = @ARGV;
#Initialize Object
$EMBOSS = new Bio::Factory::EMBOSS;
#Define emboss program to run
$application = $EMBOSS->program('matcher');
#Manipulate SeqfileA file
$seqA = new Bio::SeqIO (-file => $seqfileA,
-format => 'fasta');
while ($seqinA = $seqA->next_seq){
$inseqA = "asis::".$seqinA->seq;
$seqidA = $seqinA->id;
#$seqoutA->write_seq($inseqA);
print "####$seqidA\n";
#Initialize seqB at every iteration of SeqA
$seqB = new Bio::SeqIO (-file => $seqfileB,
-format => 'fasta');
while ($seqinB = $seqB->next_seq){
$inseqB = "asis::".$seqinB->seq; #Format like asis::ATGCGA (required
for emboss)
$seqidB = $seqinB->id;
#$seqoutB->write_seq($inseqB);
#print "####$inseqA\n";
print "Processing sequence $seqidA..vs..$seqidB...";
#Define program parameters and run...
$application->run({
-sequencea => $inseqA,
-sequenceb => $inseqB,
-outfile => $outfile });
print "done\n";
....
Manipulate alignments.....
....
}
}
-----Original Message-----
From: Peter Rice [mailto:peter.rice at uk.lionbioscience.com]
Sent: mardi, 26. novembre 2002 14:54
To: Vilanova,David,LAUSANNE,NRC/BS
Cc: 'emboss at embnet.org'
Subject: Re: Matcher
Vilanova,David,LAUSANNE,NRC/BS wrote:
> Dear all,
> I was wondering if matcher program accepts a sequence via stdin.
>
> the following exemple doesn't work for me.
>
> matcher -sequencea 'ATGCGA' -sequenceb 'ATCTAGATATGCGA'
>
>>cannot open ATGCGA file for read.
>
>
> Is there anyway to submit a sequence via stdin ???
You don't mean stdin (that can only read one sequence anyway) ... you mean
"can I specify a sequence on the command line?"
Yes!!!! You need the "asis" special format.
matcher -sequencea 'asis::ATGCGA' -sequenceb 'asis::ATCTAGATATGCGA'
(assuming your shell allows the command line to be long enough for your
sequences :-)
Hope this helps
Peter
--
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723
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